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work_log_aml
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### step 1 ###
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q dinglab --step 1
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 2
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 3
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --minvaf 0.05 --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 4
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --minvaf 0.05 --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 5
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --minvaf 0.05 --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 6
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --minvaf 0.05 --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 7 --sre 1
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --minvaf 0.05 --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 8
perl germlinewrapper.pl --rdir /scratch1/fs1/dinglab/scao/gw/cptacaml/b1 --log /scratch1/fs1/dinglab/scao/gw/cptacaml/b1.log --minvaf 0.05 --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --users songcao --groupname GermlineWXS --q general --step 9